Uncommon or Common Descent?


(Bill Cole) #21

I wonder if there are gene variations (like homoplaises between species) in species that we know are related by common descent?


(Bill Cole) #22

The fact that the dependency model fits modular software design is interesting. Winston has put a testable model together but we are in the first inning of validation as Joshua mentioned. Everyone realizes that the Common descent hypothesis is messy but it has until now been the only hypothesis on the table. Dr. Swamidass is pushing Winston to improve his model and this is a good thing.

Dr Swamidass

One question I have is how would we measure neutral mutations without an evolutionary assumption.


(S. Joshua Swamidass) #23

Great to see you @colewd. Thanks for showing yourself here and welcome. A bit busy the next few days, but will try and answer you guys as soon as I can. While I’m in out, maybe others might engage too. I’ll be back!


(Bill Cole) #24

Thanks Joshua

I look forward to continuing our discussions. This site looks far superior to BioLogos.

Best

Bill


(Eric Michael Holloway) #25

Dr. Swamidass claims this is seen in human genetic history. However, this would be an especially good piece of evidence for dependency injection/intelligent design, since humans have been intentionally breeding themselves for as long as we know.

A better piece of counter evidence would homoplaises in the absence of intention, such as in plants and in simple creatures.


(Intelligent Design Deist) #26

I repeat:

What Common Descent requires is a mechanism capable of explaining the anatomical and physiological differences observed between two allegedly related species such as chimps and humans. Right now we don’t have that. So right now the best we can do is say “we don’t know”. That is the only honest scientific answer to the question.

Dr Joshua said my statement is false but failed to explain why it is false. What is the mechanism and how can we test it, Dr Joshua?


(Bill Cole) #27

This may not be accurate. We are dealing with bits here which is an exponent 2^n. A difference to 111,111 bits means 2^111111 times more likely to be the fit then the smaller number. This is hard to imagine as we are dealing with enormous numbers to start with.

If this all is accurate then this should reject the tree, however there is a lot of work to do to validate this level of difference.


(S. Joshua Swamidass) #28

Be patient. I’m a scientist that has responsibilities to tend to also. Give it at least 1 week before repeating a question you know I’ve seen. Also do not address it to me specifically. Others can help you too.

I’ll answer it now though.

This has nothing to do with common descent. Your argument is a non-sequitur for tow reasons.

  1. Common descent does not attempt to explain the “anatomical and physiological differences” between related species. You might as well reject quantum mechanics for failing to explain the orbit of the moon around the earth.

  2. Many of mechanisms that give rise to the “anatomical and physiological differences” between different species are well known. It is an active area of research to refine our knowledge, and to continue growing it.

I understand you are unaware of #2. @T.j_Runyon can help you, and so can others, but on another thread. I’ll start it for you. That gets to a fundamental problem with your argument. It is an argument from personal ignorance. You personally don’t know of something, so you think it does not exist. To start with, we have very low expectation that you would or should know much about a complex and vast area of biology. So declaring your ignorance is not particularly effective.

Instead, phrase it in a less aggressive way, that invites others to educate you. You will learn a lot, and it will be fun. I’ll show you how to ask in the thread I set up.


Explaining Biological Differences Between Humans and Chimps
(S. Joshua Swamidass) #29

Explanations have been given in both the main thread and in my responses here and elsewhere. At some point you can engage them and ask specific questions.

We also did explain how. It is in technical language, and you might have to learn a lot of biology to grasp it. The best way to make sense of it is ask for explication of sentences that did not make sense to you. Don’t mistake difficulty in comprehending a complex field for lack of explanation. It is possible to learn this, but you have to slow down and hold back from conclusions like this.

I appreciate your honesty here. It sounds like you are saying, however, that because you do not understand something it does not exist. You can understand why no one is going to find that convincing. It is not a warranted conclusion.

Moreover, the discussion of ID is beside the point. Common descent is a design principle too. So this is not ID vs not-ID. Rather we are talking about if Ewert has identified a real pattern in the data, or not. Once we settle if he has, we have to look very carefully at realistic models of common descent (not trees), considering both known and putative mechanisms in turn. This is a massive effort. He has just begun.

Everyone agrees that trees are not a good model of common descent, and that more complex things have happened. “Dependency injection” is an imprecise term, that I think you mean to imply “design.” If that is the case, it is an unwarranted inference for several reasons.

Yes there are. Though you need to define what type of homoplaises in more detail. You can see some examples of genetic mutations here: Heliocentric Certainty Against a Bottleneck of Two?

Well said.


(S. Joshua Swamidass) #30

I’m sorry @colewd, that is not how it works. It is just as I said:

Moreover, even if it is correct, it does not deal with the strong evidence for common descent. He has a lot of work ahead of him. He is doing great, but for example, this is an example of a pattern we are much less convinced will work.

He is being honest here. Give him some space to figure it out, and also legitimize his work by acknowledging he is tackling an important and unsolved problem in ID. Let’s see how far he gets with this. Even if it ultimately does not work, we will give @Winston_Ewert credit for being honest about negative results. Maybe the next time around he will do better.


(Bill Cole) #31

Were dealing with exponents here right? This is important to nail down going forward when we are comparing probabilities. Is it 111,111 or 111,111 bits. I think it has to be bits because of the massive improbability of the null being true.

If I am right the math here clearly rejects common descent alone as the cause. Now we know anyway that there are other mechanisms that must be at play if it is not design right?

Fair enough. If you have time can you explain this issue to me in more detail?


(Intelligent Design Deist) #32

If “Common descent does not attempt to explain the “anatomical and physiological differences” between related species” then it doesn’t explain anything as it is those differences that it needs to explain.

If my argument is an “argument from personal ignorance” then it extends to the entire planet and everyone in it. For example, I was told to read “Evolution’s Witness: How the Eye Evolved” and yet there isn’t anything in the book that says how eyes/ vision system evolved. It just compared different eyes/ vision systems. The author has no idea if any amount of genetic change can produce eyes/ vision systems starting with populations that didn’t already have them.

I have read what several real scientists have said about this- including Sean Carroll’s books on developmental biology. We are just now understanding development and we don’t know how that came to be.


(T J Runyon) #33

Well, once again the evidence for common descent is independent of mechanism. It predicts patterns that doesn’t rely on mechanism. Your assertion is just false. But let’s talk mechabisms. Let’s take the popular figure of 98% similarity between us and chimps (though I think it’s actually about 95%). If each cell contains about 30 million base pairs that comes out to around 40 million differences. Now obviously all of these aren’t going to have a large impact but some will. Most of the differences can be explained by changes in gene regulation, timing, and expression. Remember it’s not what genes you have. It’s how you use the ones you do have. The same genes can do very different things when they are expressed differently


(S. Joshua Swamidass) #34

You just changed the standard, dropping the phrase “mechanism of”. That is a consequential change, but also leave the meaning unspecified. You can’t change the terms of the question in your response. Perhaps you need to clarify what exactly you are thinking first. Maybe you do have a valid point, but you are not being clear or consistent enough in your language to follow.

No, that would be an argument from ignorance, not one from personal ignorance. The fact of the matter is that was we know many of the mechanisms that give rise to differences between humans and chimps. Period.

The right way to say it is a BOTH-AND. We BOTH understand a great deal AND do not know the whole story.


(S. Joshua Swamidass) #35

10 posts were merged into an existing topic: Missing the Point on Ewert


(T J Runyon) #39

The evidence is there. The same genes are used in brain development in us, chimps, gorillas, etc. but they are expressed differently. This explains some of the differences we see


(T J Runyon) #41

I didn’t think this was controversial. I know of prominent ID proponents who grant this. I witnessed a conversation between @swamidass and one where this was discussed.


(Bill Cole) #42

You are right it on its own the only thing it explained is the hierarchal pattern in the data. This is why Behe had no time to challenge this hypothesis. Winston has shown here that design may actually fit the pattern better. The major issue is that his paper is at the very early stages of testing.

As Joshua said ID needed an alternative positive explanation and now there is a candidate to challenge the current paradigm of the cause of the pattern. He has shown that software design can create this type of pattern and is working to validate that gene families can do the same.

The devil is in the detail of how he chose the genes and the actual genes that make up the families in his paper, how similar are they? This is the challenge Joshua is putting him through.


(S. Joshua Swamidass) #43

A separate and excellent point.


(S. Joshua Swamidass) #44

Not yet. He has not demonstrated this yet.